entire enable --agent codex can create .codex/config.toml under ~/.codex/agents and trigger Codex warning

[sanogueralorenzo]

Summary

When entire enable --agent codex is run in a repository located under ~/.codex/agents/..., it creates a repo-local .codex/config.toml that Codex later interprets as an agent role file and warns about at startup.

This seems to happen because ~/.codex/agents is a reserved tree that Codex uses for agent-role discovery, and in some setups it is also used to hold git worktrees/checkouts.

Steps to reproduce

1. Create or place a git repository under a path inside ~/.codex/agents, for example:

   ~/.codex/agents/repos/project

2. In that repository, run:

   entire enable --agent codex

3. Start Codex CLI in that repository.

Actual behavior

entire enable --agent codex creates:

~/.codex/agents/repos/project/.codex/config.toml

with:

[features]
codex_hooks = true

Then Codex CLI shows this warning:

⚠ Ignoring malformed agent role definition: agent role file at ~/.codex/agents/repos/project/.codex/config.toml must define `developer_instructions`

Expected behavior

Enabling Codex hooks should not create a config file that Codex will later interpret as an agent-role definition when the repository lives under ~/.codex/agents/....

Possible fix

Enable features.codex_hooks = true in $CODEX_HOME/config.toml, or use another location that does not conflict with Codex agent-role discovery.